2.3.3.3.21. NXapm_paraprobe_clusterer_results

Status:

application definition, extends NXobject

Description:

Application definition for results files of the paraprobe-spatstat tool. ...

Application definition for results files of the paraprobe-spatstat tool.

This tool is part of the paraprobe-toolbox. Inspect the base class NXapm_paraprobe_tool_results.

Symbols:

The symbols used in the schema to specify e.g. dimensions of arrays.

n_ions: The total number of ions in the reconstruction.

n_feat: Number of clusters found.

Groups cited:

NXapm_paraprobe_tool_common, NXapm_paraprobe_tool_results, NXcoordinate_system_set, NXcoordinate_system, NXcs_filter_boolean_mask, NXcs_profiling, NXentry, NXprocess, NXprogram, NXserialized, NXsimilarity_grouping, NXuser

Structure:

ENTRY: (required) NXentry

definition: (required) NX_CHAR ⤆

Obligatory value: NXapm_paraprobe_clusterer_results

@version: (required) NX_CHAR ⤆

cameca_to_nexus: (optional) NXapm_paraprobe_tool_results

cluster_analysisID: (optional) NXapm_paraprobe_tool_results

analysis_identifier: (required) NX_UINT

config: (required) NXserialized

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

window: (required) NXcs_filter_boolean_mask ⤆

number_of_ions: (required) NX_UINT ⤆

bitdepth: (required) NX_UINT ⤆

mask: (required) NX_UINT ⤆

dbscanID: (optional) NXsimilarity_grouping

Results of a DBScan clustering analysis.

eps: (required) NX_FLOAT {units=NX_LENGTH}

The epsilon (eps) parameter used.

min_pts: (required) NX_UINT {units=NX_UNITLESS}

The minimum points (min_pts) parameter used.

cardinality: (required) NX_UINT {units=NX_UNITLESS} ⤆

Number of members in the set which is partitioned into features. ...

Number of members in the set which is partitioned into features. Specifically, this is the total number of targets filtered from the dataset, i.e. typically the number of clusters which is usually not and for sure not necessarily the total number of ions in the dataset.

identifier_offset: (required) NX_INT ⤆

Which identifier is the first to be used to label a cluster. ...

Which identifier is the first to be used to label a cluster.

The value should be chosen in such a way that special values can be resolved: * identifier_offset - 1 indicates an object belongs to no cluster. * identifier_offset - 2 indicates an object belongs to the noise category.

Setting for instance identifier_offset to 1 recovers the commonly used case that objects of the noise category get the value of -1 and points of the unassigned category get the value 0.

targets: (required) NX_UINT (Rank: 1, Dimensions: [i]) {units=NX_UNITLESS}

The evaporation (sequence) identifier (aka evaporation_id) to figure out ...

The evaporation (sequence) identifier (aka evaporation_id) to figure out which ions from the reconstruction were considered targets. The length of this array is not necessarily n_ions. Instead, it is the value of cardinality.

number_of_solutions: (optional) NX_UINT (Rank: 1, Dimensions: [i]) {units=NX_UNITLESS}

The number of solutions found for each target. Typically, ...

The number of solutions found for each target. Typically, this value is 1 in which case the field can be omitted. Otherwise, this array is the concatenated set of values of solution tuples for each target that can be used to decode model_labels, core_sample_indices, and weight.

model_labels: (optional) NX_INT (Rank: 1, Dimensions: [k]) {units=NX_UNITLESS}

The raw labels from the DBScan clustering backend process. ...

The raw labels from the DBScan clustering backend process. The length of this array is not necessarily n_ions. Instead, it is typically the value of cardinality provided that each target has only one associated cluster. If targets are assigned to multiple cluster this array is as long as the total number of solutions found and

core_sample_indices: (optional) NX_INT (Rank: 1, Dimensions: [k]) {units=NX_UNITLESS}

The raw array of core sample indices which specify which of the ...

The raw array of core sample indices which specify which of the targets are core points.

numerical_labels: (required) NX_UINT (Rank: 1, Dimensions: [k]) {units=NX_UNITLESS}

Numerical label for each target (member in the set) aka cluster identifier.

categorical_labels: (optional) NX_CHAR (Rank: 1, Dimensions: [k])

Categorical label(s) for each target (member in the set) aka cluster name(s).

weights: (optional) NX_NUMBER (Rank: 1, Dimensions: [k]) {units=NX_UNITLESS}

Weights for each target that specifies how probable the target is assign ...

Weights for each target that specifies how probable the target is assigned to a specific cluster.

For the DBScan algorithm and atom probe tomography this value is the multiplicity of each ion with respect to the cluster. That is how many times should the position of the ion be accounted for because the ion is e.g. a molecular ion with several elements or nuclides of requested type.

is_noise: (optional) NX_BOOLEAN (Rank: 1, Dimensions: [k])

Are targets assigned to the noise category or not.

is_core: (optional) NX_BOOLEAN (Rank: 1, Dimensions: [k])

Are targets assumed a core point.

statistics: (recommended) NXprocess ⤆

In addition to the detailed storage which members were grouped to which ...

In addition to the detailed storage which members were grouped to which feature here summary statistics are stored that communicate e.g. how many cluster were found.

number_of_targets: (required) NX_UINT

Total number of targets in the set, i.e. ions that were filtered ...

Total number of targets in the set, i.e. ions that were filtered and considered in this cluster analysis.

number_of_noise: (required) NX_UINT {units=NX_UNITLESS}

Total number of members in the set which are categorized as noise.

number_of_core: (required) NX_UINT {units=NX_UNITLESS}

Total number of members in the set which are categorized as a core point.

number_of_features: (required) NX_UINT {units=NX_UNITLESS}

Total number of clusters (excluding noise and unassigned).

feature_identifier: (required) NX_UINT (Rank: 1, Dimensions: [n_feat]) {units=NX_UNITLESS}

Numerical identifier of each feature aka cluster_identifier.

feature_member_count: (required) NX_UINT (Rank: 1, Dimensions: [n_feat]) {units=NX_UNITLESS}

Number of members for each feature.

common: (required) NXapm_paraprobe_tool_common

status: (required) NX_CHAR ⤆

programID: (required) NXprogram ⤆

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

profiling: (recommended) NXcs_profiling ⤆

start_time: (required) NX_DATE_TIME ⤆

end_time: (required) NX_DATE_TIME ⤆

total_elapsed_time: (required) NX_FLOAT ⤆

current_working_directory: (required) NX_CHAR ⤆

number_of_processes: (required) NX_POSINT

number_of_threads: (required) NX_POSINT

number_of_gpus: (required) NX_POSINT

userID: (optional) NXuser ⤆

If used, metadata of at least the person who performed this analysis.

name: (required) NX_CHAR ⤆

coordinate_system_set: (required) NXcoordinate_system_set ⤆

paraprobe: (required) NXcoordinate_system ⤆

type: (required) NX_CHAR ⤆

handedness: (required) NX_CHAR ⤆

x: (required) NX_NUMBER (Rank: 1, Dimensions: [3]) {units=NX_LENGTH} ⤆

y: (required) NX_NUMBER (Rank: 1, Dimensions: [3]) {units=NX_LENGTH} ⤆

z: (required) NX_NUMBER (Rank: 1, Dimensions: [3]) {units=NX_LENGTH} ⤆

Hypertext Anchors

List of hypertext anchors for all groups, fields, attributes, and links defined in this class.

NXDL Source:

https://github.com/FAIRmat-NFDI/nexus_definitions/tree/fairmat/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml